|
| Status |
Public on Jul 27, 2020 |
| Title |
RNAseq N2 36h |
| Sample type |
SRA |
| |
|
| Source name |
synchronized population
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: 36h
|
| Growth protocol |
L1 synchronized by egg prep and M9 incubation over night. A population of N2 worms was grown on OP50-containing agar plates at 25 degrees. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and conventional Phenol/choloform extraction
TruSeq-illumina-mRNA seq followed by Hiseq 50-cycle-single-end-reads on HiSeq2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
expr_mRNA_CE10_coding.tab
|
| Data processing |
RNA-seq data were mapped to the C. elegans genome (ce10) using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R.
Gene expression was quantified using qCount function from the QuasR package in R.
Counts were scaled by total mapped library size for each sample.
A pseudocount of 8 was added and counts were log2-transformed.
lowly expressed genes were excluded (maximum expression – mean-normalized log2-transformed gene width ≤ 6).
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (WormBase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.
|
| |
|
| Submission date |
May 07, 2019 |
| Last update date |
Jul 27, 2020 |
| Contact name |
Helge Grosshans |
| E-mail(s) |
helge.grosshans@fmi.ch
|
| Organization name |
Friedriche Miescher Institute for Biomedical Research (FMI)
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE130811 |
mRNA-seq time course of C. elegans sampled from 5h until 48h at 25 degrees |
| GSE133576 |
State transitions of a developmental oscillator |
|
| Relations |
| BioSample |
SAMN11586367 |
| SRA |
SRX5801488 |
